miRNA: 3'- aAAAACgGCCGUCCAU----GCUGCuGCGC- -5'
miRNA: 3'- aaaaACGGCCGu---C-CAUGCuGCUGCGC- -5'
miRNA: 3'- aaAAACGG--CCGUCC-AUGCU---------GCUGCGc -5'
miRNA: 3'- aaaaaCgGCCG----UCCAUGCuGCUGCGC- -5'
Results 21 - 24 of 24 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 22973 | 5' | -54.1 | NC_005137.2 | + | 17829 | 0.68 | 0.840281 |
|
Target: 5'- gUUUUGgUGGCAGGUAuuguUGGCGuCGUGu -3' miRNA: 3'- aAAAACgGCCGUCCAU----GCUGCuGCGC- -5' |
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| 22973 | 5' | -54.1 | NC_005137.2 | + | 10881 | 0.66 | 0.935245 |
|
Target: 5'- ---gUGCUGGCcgacGcGUGCG-CGAUGCGg -3' miRNA: 3'- aaaaACGGCCGu---C-CAUGCuGCUGCGC- -5' |
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| 22973 | 5' | -54.1 | NC_005137.2 | + | 7308 | 0.66 | 0.918909 |
|
Target: 5'- -cUUUGCCcgGGCAGGaUGCGGucaaagugcUGGCGCc -3' miRNA: 3'- aaAAACGG--CCGUCC-AUGCU---------GCUGCGc -5' |
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| 22973 | 5' | -54.1 | NC_005137.2 | + | 4599 | 0.68 | 0.848556 |
|
Target: 5'- ----cGaCGGCgcgaAGGUGCG-CGACGCGg -3' miRNA: 3'- aaaaaCgGCCG----UCCAUGCuGCUGCGC- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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